Proper folder structure and bulk renaming and moving

Okay guys, I think I realize why my tv shows are populating with individual episodes on some shows. On some shows, I have every episode in it's own folder. The reason I do this was due to subtitles. I would name the folder the same as the episode. For example: TV Shows/Title/Season/S01E01/S01E01.mkv. Plex doesn't have a problem with this. Is this something that Channels will sort itself out after a few hours of scraping, or do I need to delete that extra folder?

Now if I do have to delete that extra folder, does anyone know of a software that can sort this out for me in bulk?

So yeah, to answer my own question, that extra folder has to be deleted. Bulk Rename Utility has been a great software for me to fix my issues.

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